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‘Rise above yourself and grasp the world’ Archimedes – attribution

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Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world

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chemical-evolution-1

Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?

Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.

Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.

Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.

Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?

Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:

How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.

Jacinta: You understand that?

Canto: Sort of.

Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.

Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.

Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.

Canto: Semantics.

Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.

Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know cell membranes, proteins, ATP and the like. And people are working towards this.

Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?

Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.

Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.

Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.

fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution

Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.

Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.

Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.

Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.

Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…

Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.

Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.

Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….

Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath  the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.

a hydrothermal vent off the coast of New Zealand. Image from NOAA

a hydrothermal vent off the coast of New Zealand. Image from NOAA

Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.

Jacinta: Yes, we need to explore the exploitation of proton gradients, the development  of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.

Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.

Jacinta: Next time maybe.

 

Written by stewart henderson

July 29, 2016 at 8:51 am

the unpredictable effects of permafrost thaw

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This Aug. 12, 2009, photo shows a section of the vital Dempster Highway linking southern Canada with the Northwest Territories after it collapsed because warming temperatures caused the permafrost below to thaw. Permafrost melting from global warming is causing damage to infrastructure across the Arctic. (AP Photo/Rick Bowmer)

This Aug. 12, 2009, photo shows a section of the vital Dempster Highway linking southern Canada with the Northwest Territories after it collapsed because warming temperatures caused the permafrost below to thaw. Permafrost melting from global warming is causing damage to infrastructure across the Arctic. (AP Photo/Rick Bowmer)

Canto: So what’s on the agenda for 2016 here at the new ussr?

Jacinta: Well I’m hoping we can do a ‘deep dive’, as one researcher likes to put it, on GMOs, another polarising subject, with a few posts, and maybe at least one on Monsanto, the supposedly evil capitalist monster that the anti-GMO crowd love crusading against…

Canto: Good, and I’d also like to focus a bit more on climate change, the ever-developing science of monitoring this complex beast, as well as the clean energy responses.

Jacinta: Including nuclear?

Canto: Well of course I don’t want to shy away from its potential, or its problems.

Jacinta: So no more black holes and cosmic webs?

Canto: I’d love to cover everything, if I had but talent enough, and time.

Jacinta: Yes and I’d like to find time for some philosophy as well, say on the limits of science, if any. But okay let’s get started on climate. I know you’ve been thinking about the ‘Climate Watch’ segment in the most recent issue of  Cosmos, Australia’s most excellent science mag.

Canto: Yes, so while we’re congratulating our leaders (or not) on coming to an agreement re targets for global warming, we need to keep our eyes on the changes already underway, which many have been warning for years might lead to runaway, unstoppable warming.

Jacinta: Feedback loops and cascading effects.

Canto: Precisely, and one of the most serious, because unpredictable, changes we’re witnessing is in the arctic permafrost.

Jacinta: Which presumably is becoming less perma and frosty.

Canto: It’s thawing out, releasing large volumes of methane from the microbes that have been frozen there for many centuries.

Jacinta: And that’s a biggie in terms of greenhouse gases. So why do these presumably dead organisms release methane? I thought all our methane came from cow farts.

Canto: Did you really? Methane is released by rotting organic matter. You have peas in your freezer? Yes? So can you smell them? Very unlikely in their frozen state. So dig out a handful and stick them out in our summer sun. Pretty soon they’ll start to smell. What are you smelling?

Jacinta: Uhh, methane?

Canto: You’re quick. Amongst other gases of course – pure methane doesn’t stink like that. And because methane is such a potent greenhouse gas its release speeds up the thawing process, which could lead to a kind of tipping point, but the extent of this speeding up process, the amount of methane currently being released, and how it will affect the overall warming, these are horrendously difficult values to predict.

Jacinta: And methane’s essentially what we call natural gas isn’t it? CH4? So it’s another carbon-based product.

Canto: Yes, and twenty times more potent than CO2 as a greenhouse gas, according to climate scientists.

Jacinta: And the process we call rotting, that’s actually bacterial, isn’t it? Is it that these microbes release methane, inter alia, the way that we release CO2, after breathing in oxygen?

Canto: You’re talking about methanogens, which are actually archaea rather than bacteria. They thrive in anoxic, or low oxygen conditions, such as wetlands, but also in the digestive tracts of ruminants, indeed in most animals including humans. We release methane when we fart.

Jacinta: Some more than others. So I suppose the permafrost contains all these archaea, or they multiply when it starts to thaw?

Canto: They’re unlocked or reawakened by the thaw, and then, recent studies have shown, they can pump out methane at a phenomenal rate. And there’s a lot of permafrost involved at the moment, in land not under ice, including about half of Russia and Canada, and much of Alaska. They reckon there’s about 1.7 trillion tonnes of carbon trapped in this permafrost, twice the amount of atmospheric carbon.

Jacinta: So how much is likely to be released?

Canto: Nobody really has any idea, that’s the problem. One study has suggested that almost a tenth could be released by 2100, which doesn’t sound like much, but this effect hasn’t been factored in by the Intergovernmental Panel on Climate Change because it’s so hard to calculate – some of the microbes will be methanogens, some will be more liable to release CO2, depending on the local environments created by the thaw. Clearly it’ll be negative though, and will just add pressure and urgency to our plan to keep global warming down.

Jacinta: Yet I thought that the regions you mentioned, those permafrost regions, were full of evergreen forests – the taiga I think is the name. And they’re a carbon sink rather than a source of emissions.

Canto: You’re right, that’s another factor. In fact the taiga is a huge carbon sink, the biggest land sink on earth, but with climate change, the whole permafrost region is becoming less of a sink and more of an emitter, perhaps for the first time. The effects, as I’ve said are very difficult to predict, because the thaw is occurring at different rates, affecting different micro-climates, and with vastly different results even within metres. Being frozen has a uniform, more predictable effect. The thaw unlocks huge varieties of ecosytems – life in all its blooming buzzing confusion.

Jacinta: Well it does sound kind of fascinating in itself, apart from the disturbing effects…

Canto: Spoken like a true disinterested scientist.

permafrost thaw ponds around Hudson Bay, Canada

permafrost thaw ponds around Hudson Bay, Canada

 

Written by stewart henderson

January 9, 2016 at 9:34 am

this one’s for the birds

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clevercrow1

Canto: If anybody doesn’t appreciate the beauty and complexity and general magnificence of birds they should pee off and never darken this blog again.

Jacinta: Right. Now what brought that on, mate?

Canto: Oh just a general statement of position vis-à-vis other species. Charles Darwin, an old friend of mine, was pretty disdainful of human specialness in his correspondence, but he kept a low profile – on this and everything else – in public. I want to be a bit more overt about these things. And one of the things that really amazes me about birds, apart from their physical beauty, is how much goes on in those teeny noggins of theirs.

Jacinta: Yes, but what really brought this on? I haven’t heard you rhapsodising about birds before.

Canto: You haven’t been inside my vast noggin mate. Actually I’ve been taking photos – or trying to – of the bird life around here; magpies, magpie-larks, crows, rainbow lorikeets, honeyeaters, galahs, corellas, sulphur-crested cockies, as well as the pelicans, black swans, cormorants, moorhens, coots and mallard ducks by the river, not to mention the ubiquitous Australian white ibis and the masked lapwing.

Jacinta: Well I didn’t know you cared. Of course I agree with you on the beauty of these beasties. Better than any tattoo I’ve seen. So you’re becoming a twitcher?

Canto: I wouldn’t go that far, but I’ve been nurturing my fledgling interest with a book on the sensory world of birds, called, appropriately, Bird sense, by a British biologist and bird specialist, Tim Birkhead. It’s divided into sections on the senses of birds – a very diverse set of creatures, it needs to be said. So we have vision, hearing, smell, taste, touch, and that wonderful magnetic sense that so much has been made of recently.

Jacinta: So we can’t generalise about birds, but I know at least some of them have great eyesight, as in ‘eyes like an eagle’.

Canto: Well, as it happens, our own Aussie wedge-tailed eagle has the most acute sense of vision of any creature so far recorded.

Jacinta: Well actually it isn’t ours, it just happens to inhabit the same land-form as us.

Canto: How pedantic, but how true. But Birkhead points out that there are horses for courses. Different birds have vision adapted for particular lifestyles. The wedge-tail’s eyes are perfectly adapted to the clear blue skies and bright light of our hinterland, but think of owl eyes. Notice how they both face forward? They’re mostly nocturnal and so they need good night vision. They’ve done light-detection experiments with tawny owls, which show that on the whole they could detect lower light levels than humans. They also have much larger eyes, compared with other birds. In fact their eyes are much the same size as ours, but with larger pupils, letting in more light. They’ve worked out, I don’t know how, that the image on an owl’s retina is about twice as bright as on the average human’s.

Jacinta: So their light-sensitivity is excellent, but visual acuity – not half so good as the wedge-tailed eagle’s?

wedge-tailed eagle - world's acutest eyes

wedge-tailed eagle – world’s acutest eyes

Canto: Right – natural selection is about adaptation to particular survival strategies within particular environments, and visual acuity isn’t so useful in the dark, when there’s only so much light around, and that’s why barn owls, who have about 100 times the light-sensitivity of pigeons, also happen to have very good hearing – handy for hunting in the dark, as there’s only so much you can see on a moonless night, no matter how sensitive your eyes are. They also learn to become familiar with obstacles by keeping to the same territory throughout their lives.

face of a barn owl - 'one cannot help thinking of a sound-collecting device, quoth researcher Masakazu Konishi

face of a barn owl – ‘one cannot help thinking of a sound-collecting device’, quoth researcher Masakazu Konishi

Jacinta: So they don’t echo-locate, do they?

Canto: No, though researchers now know of a number of species, such as oilbirds, that do. Barn owls, though, have asymmetrical ear-holes, one being higher in the head than the other, which helps them to pinpoint sound. It was once thought that they had infra-red vision, because of their ability to catch mice in apparently total darkness, but subsequent experiments have shown that it’s all about their hearing, in combination with vision.

Jacinta: Well you were talking about those amazing little brains of birds in general, and I must say I’ve heard some tales about their smarts, including how crows use cars to crack nuts for them, which must be true because it was in a David Attenborough program.

Canto: Yes, and they know how to drop their nuts near pedestrian crossings and traffic lights, so they can retrieve their crushed nuts safely. The genus Corvus, including ravens, crows and rooks, has been a fun target for investigation, and there’s plenty of material about their impressive abilities online.

seeing is believing

seeing is believing

Jacinta: So what other tales do you have to tell, and can you shed any light on how all this cleverness comes in such small packages?

Canto: Well Birkhead has been studying guillemots for years. These are seabirds that congregate on cliff faces in the islands around Britain, and throughout northern Europe and Canada. They’re highly monogamous, and get very attached to each other, and thereby hangs another fascinating tale. They migrate south in the winter, and often get separated for lengthy periods, and it’s been noted that when they spot their partner returning, as a speck in the distance, they get highly excited and agitated, and the greeting ceremony when they get together is a joy to behold, apparently – though probably not as spectacular as that of gannets. Here’s the question, though – how the hell can they recognise their partner in the distance? Common guillemots breed in colonies, butt-to-butt, and certainly to us one guillemot looks pretty well identical to another. No creature could possibly have such acute vision, surely?

Jacinta: Is that a rhetorical question?

Canto: No no, but it has no answer, so far. It’s a mystery. It’s unlikely to be sight, or hearing, or smell, so what is it?

Jacinta: What about this magnetic sense? But that’s only about orientation for long flights, isn’t it?

Canto: Yes we might discuss that later, but though it’s obvious that birds are tuned into their own species much more than we are, the means by which they recognise individuals are unknown, though someone’s bound to devise an ingenious experiment that’ll further our knowledge.

Jacinta: Oh right, so something’s bound to turn up? Actually I wonder if the fact that people used to say that all Chinese look the same, which sounds absurd today, might one day be the case with birds – we’ll look back and think, how could we possibly have been so blind as to think all seagulls looked the same?

Canto: Hmmm, I think that would take a lot of evolving. Anyway, birds are not just monogamous (and anyway some species are way more monogamous than others, and they all like to have a bit on the side now and then) but they do, some of them, have distinctly sociable behaviours. Ever heard of allopreening?

Jacinta: No but I’ve heard the saying ‘birds of a feather flock together’ and that’s pretty sociable. Safety in numbers I suppose. But go on, enlighten me.

Canto: Well, allopreening just means mutual preening, and it usually occurs between mates – and I don’t mean in the Australian sense – but it’s also used for more general bonding within larger groups.

Jacinta: Like, checking each other out for fleas and such, like chimps?

Cant: Yeah, though this particular term is usually reserved for birds. Obviously it serves a hygienic purpose, but it also helps calm ruffled feathers when flocks of colonies live beak by jowl. And if you ever get close enough to see this, you’ll notice the preened bird goes all relaxed and has this eyes half-closed, blissed-out look on her face, but we can’t really say that coz it’s anthropomorphising, and who knows if they can experience real pleasure?

Jacinta: Yes, I very much doubt it – they can only experience fake pleasure, surely.

Canto: It’s only anecdotal evidence I suppose, but that ‘look’ of contentment when birds are snuggling together, the drooping air some adopt when they’ve lost a partner, as well as ‘bystander affiliation’, seen in members of the Corvus genus, all of these are highly suggestive of strong emotion.

Jacinta: Fuck it, let’s stop beating about the bush, of course they have emotions, it’s only human vested interest that says no, isn’t it? I mean it’s a lot easier to keep birds in tiny little cages for our convenience, and to burn their beaks off when they get stressed and aggressive with each other, than to admit they have feelings just a bit like our own, right? That might mean going to the awful effort of treating them with dignity.

Canto: Yyesss. Well on that note, we might make like the birds and flock off…

how the flock do they do that?

how the flock do they do that?

Written by stewart henderson

November 13, 2015 at 12:06 pm

exoplanets – an introduction of sorts

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future_habitable_exoplanets

Jacinta: So do you think we’ve hauled ourselves out of ignorance sufficiently to have a halfway stimulating discussion on exoplanets?

Canto: I think we should try, since it’s one of the most exciting and rapidly developing fields of inquiry at the moment.

Jacinta: And that’s saying something, what with microbiomes, homo naledi, nanobots and quantum biology…

Canto: Yes, enough to keep us chatting semi-ignorantly to the end of days. But let’s try to enlighten each other on exoplanets…

Jacinta: Extra solar planets, planets orbiting other stars, the first of which was discovered just over 20 years ago, and now, thanks largely to the Kepler Space Observatory, we’ve discovered thousands, and future missions, using TESS and the James Webb telescope, will uncover megatonnes more.

Canto: Yes, and you know, about the Kepler scope, l was blown away – this might be veering off topic a bit, but I was blown away in researching this by the fact that Kepler orbits the sun. I mean, I knew it was a space telescope, but I just assumed it was in orbit around earth, probably at a great distance to avoid interference from our atmosphere, but that we can position satellites in orbit around the sun, that really sort of stunned me, more I think than the exoplanet discoveries. Am I being naive?

Jacinta: No, not at all. Well, yes and no. Everything is stunning if you haven’t followed the incremental steps along the knowledge pathway. I mean, if you think, hey the sun’s a way away, and it’s really big and dangerous, best not go there, or something like that, you might be shocked, but think about it, we’ve been sending satellites around the earth for a long time now, and we know how to do it because we know about earth’s gravitational field and can calculate precisely how to harness it for satellite navigation. We’ve currently got a couple of thousand human-made satellites orbiting the earth and trying more or less successfully to avoid colliding with each other. So the sun also has a gravitational field and we’ve known the mathematics of gravitational fields since Newton. It’s the same formula for a star, a planet or whatever, all you need to know is its mass and its radius. And look at all the natural objects orbiting the sun without a problem. Can’t be that hard.

Canto: Okay… so how do we know the mass of the sun? Okay, forget it, let’s get back to exoplanets. What’s the big fuss here? Why are we so dead keen on exploring exoplanets?

Jacinta: Well the most obvious reason for the fuss is SETI, the search for extra-terrestrial intelligence, but to me it’s just satisfying a general curiosity, or you might say a many-faceted curiosity. And it’s all about us mostly. For example, is the solar system that we inhabit typical? We’ve mostly thought it was but we didn’t have anything to compare it with, but now we’re discovering all sorts of weird and wonderful planetary systems, and star systems, with gas giants like Jupiter orbiting incredibly close to their stars – it’s completely overturned our understanding of how planets exist and are formed, and that’s fantastically exciting.

Canto: So you say we discovered the first exoplanet about 20 years ago, and now we know about thousands – that’s a pretty huge expansion of our knowledge, so how come things have changed so fast? You’ve mentioned new technologies, new space probes, why have they suddenly become so successful?

Jacinta: Well I suppose it’s been a convergence of developments, but let’s go back to that first discovery, back in 1992. Two planets, the first ever discovered, were found orbiting a pulsar – a rapidly rotating neutron star. First discovery, first surprise. Pulsars with planets orbiting them, who would’ve thought? Pulsars are the remnants of supernovae – how could planets have survived that? But that first discovery was largely a consequence of our ability to measure, and the fact that pulsars pulse with extreme regularity. Any anomaly in the pulsing would be cause for further investigation, and that’s how the planets were found, and later independently confirmed. Now this was big news, in a field that was already becoming alert to the possibility of exoplanets, so you could say it opened the floodgates.

Canto: Really? But they didn’t discover any more for two or three years.

Jacinta: Well, okay it opened the gates but it didn’t start the flood, that really happened with the second discovery, the first discovery of a planet orbiting a main-sequence star like ours.

Canto: Main sequence? Please explain?

Jacinta: Well these are stars in a stable state, a state of balance or equilibrium, fusioning hydrogen – basically stars not too different from our own, within much the same range in terms of mass and luminosity. So 51 pegasus b was the first planet to be discovered by the radial velocity method, and radial velocity means the speed at which a star is moving towards or away from us. We can measure this, and whether the star is accelerating or decelerating in its movement, by means of the Doppler effect – waves bunch up when the object emitting them is moving towards us, they spread out when the object is receding from us, and the degree of the bunching or the spreading is a measure of their speed and whether it’s accelerating or decelerating. Now we can measure this with extreme accuracy using spectrometers, and that includes any perturbations in the star’s movement caused by orbiting bodies. That’s how 51 pegasus b was discovered.

Canto: So… how long have we had these spectrometers? Were they first developed in the nineties, or to the level of accuracy that they could detect these perturbations?

Jacinta: Well I don’t have a precise answer to that apart from the general observation that spectroscopes are getting better, and more carefully targeted for specific purposes. The French ELODIE spectrograph, for example, which was used to find 51 pegasus b, was first deployed in 1993 specifically for exoplanet searching, and since then it’s been replaced by another improved instrument, but of the same type. So it’s a kind of non-vicious circle, research leads to new technology which leads to new research and so on.

doppler1

Canto: So – we’ve gotten very good at measuring perturbations in a star’s regular movements…

Jacinta: Regular perturbations.

Canto: And we know somehow that these are caused by planets orbiting around them? How do we know this?

Jacinta: Well we will know from the size of the perturbation and its regularity that it’s an orbiting body, and we know it’s not a star because it’s not emitting any light (though it may be a low-mass star whose light isn’t easily separated from its parent star). We also know – we knew from the results that it was a massive planet orbiting very close to its star – a hot Jupiter as they  call it. And that was another surprise, but we’ve developed different techniques for discovering these things and we often use them to back each other up, to confirm or disconfirm previous findings. The ELODIE observation of 51 pegasus b was confirmed within a week of its announcement by another instrument, the Hamilton spectrograph in California. So there’s a lot of confirmation going on to weed out false positives.

Canto: So radial velocity is one technique, and obviously a very successful one as it got everyone excited about exoplanets, but what others are there, and which are the most successful and promising?

Jacinta: Well the radial velocity method was initially the most successful as you say, and hundreds of exoplanets have been discovered that way, but this method actually led to a kind of bias in the findings, because it was only able to detect perturbations above a certain level, so it was best for finding large planets close to their stars. But of course that was good too because we had never imagined that large gassy planets could exist so close to their stars. It’s opened up the whole field of planet formation. Then again, if the main aim is to find earth-like planets, this method is less effective than other methods. So let’s move on to the Kepler project. Kepler was launched in 2009, and since then you could say it has blitzed the field in terms of exoplanet detection. It uses transit photometry, which means that it measures the dimming of the light from a star when an orbiting planet passes between it and the Kepler detector.

Canto: So I get the idea of transit, as in the transit of venus, which we can see pretty clearly, but it’s amazing that we can detect transiting planets attached to stars so many light years away.

Jacinta: Well this is how we’ve expanded our world, from the infinitesimally small to the unfathomably large, from multiple billions of years to femtoseconds and beyond, through continuously refining technology, but let’s get back to Kepler. It orbits around the sun, and has collected data from around 145,000 main sequence stars in a fixed field of view – stars that are generally around the same distance from that dirty big black hole at the centre of our galaxy as our sun is.

Canto: Is that significant – that we’re focusing on stars in that range?

Jacinta: Apparently so, at least according to the Rare Earth Hypothesis, which puts all sorts of unimaginative limits on the likelihood of earth-like planets, IMHO, but no matter, it’s still a vast selection of stars, and we’ve reaped a grand harvest of planets from them – some 3000-odd, with over 1000 confirmed.

Canto: So… promising earth-like planets?

Jacinta: Yes, but I must point out that earth-like planets are difficult to detect. You see, Kepler was a kind of experiment, and we’ve learned from it, so that our next project will be much improved. For various reasons due to the photometric precision of the instrument, and inaccurate estimates of the variability of the stars in the field of view, we found that we needed to observe more transits to be sure we’d detected something. In other words we needed a longer mission than we’d planned for. And of course, Kepler has suffered serious technical problems, especially the failure of two reaction wheels, which have affected our ability to repoint the instrument. Having said that, we’ve been more than happy with its success.

Canto: Okay I just want to talk about these exoplanets. Can you summarise the most interesting discoveries?

Jacinta: Well, Kepler has certainly corrected the view we might’ve gotten from the earlier radial velocity method that large Jupiter-like planets are more common than smaller ones. We’ve had a number of reports from the Kepler group over the years, and over time they’ve adjusted downwards the average mass of the planets detected. And yes, they’ve discovered a number of planets in the ‘habzone’ as they call it. But that’s not all – only this year NASA confirmed the existence of five rocky planets, smaller than earth, orbiting a star that’s over 11 billion years old. I’m just trying to give you an idea of the explosion of findings, whether or not these planets contain life. And we’ve only just begun our hunt, and the refinement of instruments. It’s surely a great time to study astrophysics. It’s not just SETI, it’s about the incredible diversity of star systems, and working out where we fit into all this diversity.

ExoplanetDiscoveries-Histogram-20140226

Canto: Okay, I can see this an appropriately massive subject. Maybe we can revisit it from time to time?

Jacinta: Absolutely.

Some very useful sites:

http://www.planetary.org/explore/space-topics/exoplanets/

http://www.smithsonianmag.com/science-nature/how-do-astronomers-actually-find-exoplanets-180950105/?no-ist

https://en.wikipedia.org/wiki/Kepler_(spacecraft)

 

Written by stewart henderson

October 30, 2015 at 10:05 pm

how did life begin?: part 2 – RNA, panspermia, viroids and reviving the blob

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1280px-Difference_DNA_RNA-EN

Jacinta: So you’re going to talk about RNA, I know that stands for ribonucleic acid, and DNA is deoxy-ribonucleic acid, so – RNA is DNA without the oxygen?

Canto: Uhhh, you mean DNA is RNA without the oxygen.

Jacinta: Whatever, they’re big complex molecules aren’t they, but RNA is simpler, and less stable I think.

Canto: Okay, I’ll take it from here. We haven’t really known for very long that DNA is the essential material for coding and replicating life, and it’s a very complex molecule made up of four chemical bases, adenine, guanine, thymine and cytosine, better known as A, G, T and C. They connect to form base pairs, A always pairing with T and C with G.

Jacinta: What the hell are chemical bases? Do you mean bases as opposed to acids?

Canto: Well, yes. These bases, also called nucleobases, accept hydrogen ions, which have a positive charge. It’s all about pair bonding. The nucleobases – A, G, C and T, as well as uracil, found in RNA – are nitrogen-containing compounds which are attached to sugars… but let’s not get bogged down too much. The point is that DNA and RNA are nucleic acids that code for life, and most of the researchers chasing down the origin of life believe that RNA is a precursor of DNA in the process of replication.

Jacinta: And presumably there are precursors to RNA and so on.

Canto: Well presumably, but let’s just look at RNA, because we have a fair amount of evidence that this molecule preceded DNA as a ‘life-engine’, so to speak, and really no solid evidence, that I know of, of anything before RNA.

Jacinta: Okay so what is this evidence, and why did DNA take over?

Canto: Right, now the subject we’re entering into here is abiogenesis, the process by which life emerged from the inanimate. RNA is probably well down the chain from this emergence, but better to start with it than to dive into speculation. Now as you probably know, RNA has a single helical structure, and today it’s heavily involved in the process whereby DNA ‘creates’ proteins. In fact, all current life forms involve the action and interaction of three types of macromolecule, DNA, RNA and proteins…

Jacinta: But of course these complex molecules didn’t spring from nowhere.

Canto: Well we don’t know how they were built up, and many pundits think they may have been seeded here from elsewhere during the late heavy bombardment, which came to an end about 3.8 billion years ago, around the time that those Greenland rocks, with their heavy load of organic carbon, have been dated to. It seems plausible considering how quickly life seems to have taken off here.

Jacinta: Okay so tell us about RNA, how does it relate to the other two macromolecules?

Canto: Well, RNA is able to store genetic information, like DNA, and in fact it’s the genetic material for some of our scariest viruses, such as ebola, SARS, hep C, polio – not to mention influenza.

Jacinta: Wow, I didn’t know that. But one thing I do know about viruses is that they can’t exist independently of a host, so is RNA the basis of any truly independent life forms?

Canto: Not currently, on our planet, as far as we know, but the evidence is fairly strong that RNA has been central to life here from the very beginning, as it is still key to the most basic components of cells such as ribosomes, ATP and other co-enzymes. This suggests that RNA was once even more central, but in some areas it’s been subordinated to, and harnessed to, the more complex and recent DNA molecule. But, yes, since we can’t look at RNA coding for independent life-forms, we need to wind the clock back still further to look at precursors and other constituents of life, such as amino acids and peptides.

Jacinta: Which are chemical molecules, not biological ones. It seems to me we’re still a long way from working out the leap from chemistry to biology.

a peptide or amide bond - a covalent bond between two amino acid molecules

a peptide or amide bond – a covalent bond between two amino acid molecules

Canto: Yes, yes but we’re bridging various gaps. Peptides are created from amino acids, as you know. They are chains of amino acids linked by peptide bonds, and proteins are only distinguished from peptides in that they’re bigger versions of them, and bonded in a particular biologically useful way. You’ll notice when you read about this stuff that the terms ‘chemistry’ and ‘biology’ are used rather arbitrarily – a chemical compound can be referred to as a biological compound and vice versa. But various experiments have cast light on how increasingly ‘biological’ constituents are formed from simpler elements. For example, you may know that meteorites and comets, which bombarded the early earth in great numbers, contained plenty of amino acids – we’ve counted more than 70 different amino acids derived from meteorites, such as the Murchison meteorite that landed in Victoria in 1969. Another probable source of these amino acids, and even more complex and ‘biological’ molecules is comets, which also contain a lot of water in frozen form, but this has raised the question of how these molecules could have survived the impact of these colossal objects, which released enormous energy, some of them partially vaporising the earth’s crust. But an ingenious experiment, described in this video, and elsewhere, was able to simulate a comet’s impact, creating pressures many times greater than that experienced in our deepest oceans, to see what would happen to the amino acids. It was expected that they would barely survive the impact, but surprisingly they not only survived but forged bonds that created complex peptides.

a fragment of Murchison meteorite - of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

a fragment of Murchison meteorite – of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

Jacinta: Mmmm, that is interesting. So, the gap between peptides, or proteins, and RNA, what do we know about that?

Canto: Well, now you’re getting into highly speculative territory, but it’s certainly worth speculating about. Firstly, though, in trying to solve this origin of life problem, we have to note that the earth’s atmosphere was incredibly different from what it is now. In fact it was probably quite different from the way Haldane and Oparin and later Miller and Urey envisaged it. It was predominantly carbon dioxide, with hydrogen sulphide, methane and other unpleasant gases – unpleasant to us, that is. That, together with the continual bombardment from outer space has led some scientists to suggest that the place to find the earliest life forms isn’t the open surface but in hidden nooks and crannies or deep underground, in more protected environments.

Jacinta: Yeah the discoveries of so-called extremophiles has made that idea fashionable, no doubt, but presumably these extremophiles are all DNA-based, so I don’t see how investigating them will answer my question.

Canto: Okay, so it’s back to RNA. The thing is, I don’t want to go into the properties of RNA here, it’s just too complicated.

Jacinta: I believe it was Richard Feynman who said something like ‘to fully understand a thing you have to build it’. So there’s still this leap from polypeptides or proteins, which don’t code for anything, they’re just built by ribosomes – RNA structures – from DNA instructions, to sophisticated coded replicators. We have no idea how DNA or RNA came into being, and nobody has successfully created life apart from Doktor Frankenstein. So it’s all a bit disappointing.

Canto: You must surely be joking, or just playing devil’s advocate. You know very well that this is an incredibly difficult nut to crack, and we’ve made huge progress, new discoveries are being made all the time in this field.

Jacinta: Okay, impress me.

Canto: Well, only this year NASA scientists have reported that the nucleobases uracil, thymine and cytosine, essential ingredients of DNA and RNA, have been created in the laboratory, from ingredients found only in outer space – for example pyramidine, which they’ve hypothesised was first created in giant red stars – and they’ve found pyrimidine in meteors. So, another step towards creating life, and further evidence that life here may have been seeded from elsewhere. And if that doesn’t impress you, what about viroids?

Jacinta: Uhhh… what are they, viral androids? Which reminds me, what about the artificial intelligence route to creating life? Intelligent life, what’s more exciting.

Canto: Another time. Viroids are described as ‘sub viral pathogens’. We were talking about viruses before, as a kind of halfway house between the living and the lifeless, but really they’re much more on the side of the living. The smallest known pathogenic virus is over 2000 nucleobases long, and the biggest – well, a megavirus was famously identified just last year and revived after being frozen in Siberian permafrost for something like 35,000 years…

Jacinta: An ancient megavirus has been revived…? WTF? Who thought that was a great idea? Wait a minute, the Siberian permafrost, wasn’t that where Steve MacQueen and his mates dropped The Blob? Megadeath, not just a shite band! We’re doomed!

Canto: Well, strictly speaking it’s a virion, a virus without a host, which means it’s in a kind of dormant phase, like a seed. But I don’t want to talk about megaviruses, fascinating though they are – and very new discoveries. I want to talk about viroids, which are plant pathogens. They consist of short strands of RNA, only a few hundred nucleases long, without the protein coat that characterises viruses, and their existence tends to support the ‘RNA world hypothesis’. It was the discoverer and namer of viroids, Theodor Diener, who pointed out that they were vitally important macromolecules for explaining essential steps in the evolution of life from inanimate matter. That was back in 1989, but his remarks were ignored, and only rediscovered in 2014. So viroids are now a big focus in abiogenesis. They’ve even been called living relics of the pre-cellular RNA world.

Viroid

Jacinta: Okay, I’m more or less impressed. We’ll have to do more on abiogenesis in the future, it’s an intriguing topic, with more breakthroughs in the offing it seems. ..

 

 

Written by stewart henderson

September 28, 2015 at 11:23 pm

how did life begin? part 1 – Greenland rocks, warm little ponds and unpromising gunk

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the basics of the Miller-Urey experiment: sparking interest

the basics of the Miller-Urey experiment: sparking interest

 

Jacinta: Well, we need an antidote to all that theological hocus-pocus, so how about a bit of fundamental science for dummies?

Canto: Sounds great, I just happened to read today that there are three great questions, or areas of exploration for fundamental science. The origin of the universe – and its composition, including weird black holes, dark matter and dark energy – that’s one. The others are the origin of life and the origin of consciousness. Take your pick.

Jacinta: I’ll choose life thanks.

Canto: Not a bad choice for a nihilist. So life has inhabited this planet for about three and a half billion years, or maybe more, while the planet was still cooling from its formation…

Jacinta: Isn’t it still doing that?

Canto: Well, yes of course. An interesting study conducted a few years ago found that around 54% of the heat welling up from within the earth is radiogenic, meaning that it results from radioactive decay of elements like radium and thorium. The rest is primordial heat from the time of the planet’s coalescing into a big ball of matter.

Jacinta: Gravity sucks.

Canto: Energetically so.

Jacinta: You say three and a half billion years or more – can you be a bit more specific? Are we able to home in on the where and the when of life’s origin on this planet?

Canto: Well, that would be the pot of gold, to locate the place and time of the first homeostatic replicators, to wind back history to actually witness that emergence, but I suspect there would be nothing to actually see, at least  not on the time-scale of a human life. I think it’d be like the emergence of human language, only slower. You’d have to compress time somehow to witness it.

Jacinta: Fair enough, or maybe not, it seems to me that the distinction between the animate and the inanimate would be pretty clear-cut, but anyway presumably scientists have a time-frame on this emergence. What allows them to date it back to a specific time?

Canto: Well, it’s an ongoing process of honing the techniques and discovering more bits of evidence, a bit like what has happened with defining the age of our universe. For example, you’ve heard of stromatolites?

Jacinta: Yes, those funny black piles that stick out of the water and sand, somewhere in Western Australia? They’re made from really old fossilised cyanobacteria, right?

Canto: Well, that’s a start, they’re rather more complicated than that and we’re still learning about them and still discovering new deposits, all around the world, both on the shoreline and inland. But the Shark Bay stromatolites  in WA were the first to be identified, and that was only in 1956. More recently though, there’s been an entirely different discovery in Greenland that’s raised a lot of excitement and controversy…

Jacinta: But hang on, these stromatolites, they say they’re really old, like more than 3 billion years, but how do they know that? As Bill Bryson would say.

Canto: Well, good question Jass, in fact it’s highly relevant to this Greenland discovery so let me talk about radiometric dating, using this example. Greenland has been attracting attention since the sixties as a potential mineral and mining resource, so the Danish Geological Survey was having a look-see around the region of Nuuk, the capital, in the south-west of the island. The principal geologist found ten successive layers of rock in the area, using standard stratigraphic techniques that you can find online, though they’re not always easy to apply, as strata are rarely neatly horizontal, what with crustal movements, fault-lines and rockfalls and erosion and such. Anyway, it was his educated guess that the bottom of these layers was extremely old, so he sent a sample to Oxford, to an expert in radiometric dating there. This was in about 1970.

Isua rocks, Greenland. Oldest rocks discovered, showing plausible traces of 3.8 billion-year-old life

Isua rocks, Greenland. Oldest rocks discovered, showing plausible traces of 3.8 billion-year-old life

Jacinta: And doesn’t it have to do with radioactive isotopes and half-lives and such?

Canto: Absolutely. Take uranium 238, which if you’ve been watching the excellent recent ABC documentary you’ll know that it decays through a whole chain of, from memory, twelve nuclides before stabilising as an isotope of lead. That decay has a half-life of 4.5 billion years – longer than the life of this planet, or at least the life of its crust. So it’s a matter of measuring the ratio of isotopes, to see how much of the natural uranium has decayed. In this case, the gneiss, the piece of bottom-strata rock that was analysed, had the highest proportion of lead in it of any naturally occurring rock ever discovered.

Jacinta: So that means it’s likely the oldest rock? Aw, I thought Australia had the oldest. This is terrible news.

Canto: No time to be parochial when the meaning of life is at stake. May I continue? So this was an exciting discovery, but more was to come, and it’s continuing to come. The geological team were inspired to continue their explorations around the Godthaab Fjord in Greenland, and found what are called ‘mud volcanoes’, pillows of basaltic volcanic lava that had issued out into the seawater. These were again dated at about 3.7 billion years old, and this strongly suggested the existence of warm oceans at that time, with hydrothermal vents such as those recently discovered to be teeming with life…

Jacinta: Right, so that might be pushing the age of life back a few hundred million years, if it can be verified, but it still doesn’t answer the how question..

Canto: Oh, nowhere near it, but I’ve just started mate. May I continue? Not surprisingly this region is now seen as a treasure trove for those hunting out the first life forms and trying to work out how life began. It was soon found that the Isua greenstone to the north of Nuuk contains carbon with a scientifically exciting isotopic ratio. The level of carbon 13 was unexpectedly low. This is generally an indication of the presence of organic material. Photosynthesising organisms prefer the lighter carbon 12 isotope, which they capture from atmospheric or oceanic carbon dioxide. But the finding’s controversial. Many are skeptical because this is the period known as the ‘late heavy bombardment’, with asteroids crashing and smashing and vaporising and possibly even sterilising… and they haven’t discovered any fossils.

Jacinta: So, photosynthesis, that’s what created the great oxygenation, which created an atmosphere for complex oxygen-dependent organisms, is that right?

Canto: Well, that was much later, and it’s a vastly complex story with quite a few gaps in it, so maybe we’ll save it for future conversations…

Jacinta: Okay, fine, but couldn’t one of those asteroids have brought life here, or proto-life, or the last essential ingredient…?

Canto: Yes, yes, maybe, but you’re distracting me. May I please continue? Where was I? Okay, so let’s look at the various theories put forward about the origin of life – and it will bring us back to Greenland. You’ve mentioned one, called panspermia. That’s the idea that life was seeded here from space, maybe during the heavy bombardment…

Jacinta: Which isn’t an adequate explanation at all, because where did that life come from? I want to know how any life-form anywhere can spring from the inanimate.

Canto: Yes all right, don’t we all smarty-pants? One of the most interesting early speculators on the subject was one Charles Darwin, who wrote – very famously – in a letter to his good mate Joseph Hooker in 1871, and I quote:

It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present.— But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.

Now this was pretty damn good speculation for the time, and a couple of generations later two biologists, Aleksandr Oparin of Russia and John Haldane of England, independently developed a hypothesis that built on Darwin’s ideas.

Jacinta: Oh yes, they had this idea that if you added a bit of lightning to the early terrestrial atmosphere, which was full of  ammonia or something, you’d get a lot of organic chemistry happening.

Canto: Well I think the ‘or something’ part is true there – their idea was that there was a lot of hydrogen, methane and water vapour in the early atmosphere, and that, combined with local heat caused perhaps by lightning, or volcanic activity or some sort of concentrated solar radiation, the combo created a soup of organic compounds, out of which somehow over time emerged a primordial replicator.

Jacinta: So far, so vague.

Canto: Okay, I’m just getting started. The Oparin-Haldane hypothesis was highly speculative, of course. The point being made was that this key event was all that was needed for natural selection to kick in. This replication must have been advantageous, and of course over time there would’ve been mutations,with the mutants competing with the originals, and the winners would’ve been the most efficient and effective harvesters of resources, and there would’ve been expansion and more mutations and modifications and so forth. And out of that would come the first self-sustaining homeostatic environment, the proto-cell, within which more sophisticated machinery for processing resources could be developed…

Jacinta: Okay so you’ve more or less succeeded in dissolving the boundary between the animate and the inanimate before my eyes, but it’s still pretty vague on the details.

Canto: In 1953, Stanley Miller took up the challenge of his supervisor, famous Nobel Prize-winning biologist Harold Urey, who noted that nobody had tested the Oparin-Haldane hypothesis experimentally. Miller created a mini-atmosphere in a bottle, using methane (CH4), hydrogen, water vapour and ammonia (NH3), and after sparking it up for a while, he managed, to the amazement of all, to produce amino acids, the building blocks of proteins. Surely the first step in producing life itself.

Jacinta: Ah yes, that was a famous experiment, but didn’t it turn out to be something of a dead end?

Canto: Well, yes and no. It has been replicated with different mixtures and ratios of gases, and amino acids, sugars and even traces of nucleic acids have been generated, but nothing that could be described as a primordial replicator. But of course this work has got a lot of biologists thinking.

Jacinta: But this was 60 years ago. That’s a lot of thought without much action.

Canto: Well, what has since been realised about the experiments of Miller and others is that they create an enormous complexity of organic molecules in a rather uncontrolled way, a kind of chemical gunk similar to what might be created when you burn the dinner. The point being that when you burn the dinner – which is something necessarily organic like a dead chook, or pig, or tragically finless shark or whatnot…

Jacinta: Or a pumpkin, or Nan’s rhubarb pie..

Canto: Yeah, okay – you get this messy complexity, all mixed with oil and vinegary acids and shite – you get this break-down into gunk, and that’s easy. What’s hard is to go in the other direction, to build up from gunk into a fully fledged chicken, or a handsomely finned shark. And that’s what these experiments were trying to do, in their small way. They were creating this primordial-soup-gunk and hoping, with a bit of experimental help, to spark life into it, and basically getting nowhere. The problem is essentially to do with randomness and order. How do we get order out of random complexity? It’s easy to go the other way, for example with explosions and machine guns and such. We see that everywhere. But building the kind of replicating order that you find even in mycoplasma, the smallest genus of bacteria, from scratch, and by chance – well, that’s mind-bogglingly improbable.

mycoplasma, one of the simplest life forms - but try making one from scratch

mycoplasma, one of the simplest life forms – but try making one from scratch

Jacinta: So we have to think in terms of intermediate stages.

Canto: Yes, well, there are big problems with that, too… But let’s give it a rest for now. Next time, we’ll discuss the RNA world that most biologists are convinced preceded and helped create the DNA world we live in.

 

N B – This piece owes much to many, but mainly to Life on the edge: the coming of age of quantum biology, by Jim Al-Khalili & Johnjoe McFadden

Written by stewart henderson

September 8, 2015 at 10:03 pm

the anthropic principle lives on and on

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Believable-Creationism24c

The anthropic principle, the idea that the universe – and let’s not muddle up our heads with multiverses – appears to be tweaked just right, in a variety of ways, for the existence and flourishing of humans, has long been popular with the religious, those invested in the idea of human specialness, a specialness which evokes guided evolution, both in the biological and the cosmological sense. And, of course, God is our guide.

Wikipedia, God bless it, does an excellent job with the principle, introducing it straight off as the obvious fact that anyone able to ascertain the various parameters of the universe must necessarily be living in a universe, or a particular part of it, that enables her to do the ascertaining. In other words the human specialness mob have it arse backwards.

So I’ll happily refer all those questing to understand the anthropic principle, in strong and weak forms, it proponents and critics, etc, to Wikipedia. I’ve been brought to reflect on it again by my reading of Stephen Jay Gould’s essay, ‘mind and supermind’, in his 1985 collection, The Flamingo’s Smile. 

Yes, the anthropic principle, which many tend to think is a clever new tool for deists, invented by the very materialists who dismiss the idea of supernatural agency as unscientific, is an old idea – much more than 30 years old, because Gould was critiquing not only Freeman Dyson’s reflections on it in the eighties, but those of Alfred Russel Wallace more than a century ago, in his 1903 book Man’s Place in the Universe. Gould had good reason for comparing Dyson and Wallace; their speculations, almost a century apart, were based on vastly different understandings of the universe. It reminds us that our understanding of the universe, or that of the best cosmologists, continues to develop, and, I strongly suspect, will never be settled.

Theories and debates about our universe, or multiverse, its shape and properties, are more common, and fascinating, than ever, and accompanied by enough mathematics to make my brain bleed. The other day one of my regular emails from Huff Po science declared that maybe the universe didn’t have a beginning after all. This apparently from some scientists trying to grab attention in a pretty noisy field. I’ve only scanned the piece, which I would hardly be qualified to pass judgment on. But not long ago I read The Unknown Universe, a collection of essays from New Scientist magazine, dedicated to all ideas cosmological. I didn’t understand all of it of course, but genuine questions were raised about whether the universe is finite or infinite, about whether we really understand the time dimension, about how the laws that govern the universe came into being, and many other fundamental concepts. It’s interesting then to look back to more than a century ago, before Einstein, quantum mechanics, and space probes, and to reflect on the scientific understanding of the universe at that time.

A version of the universe, based on Lord Kelvin's calculations, used by Wallace

A version of the universe, based on Lord Kelvin’s calculations, used by Wallace

In Wallace’s time (a rather vague term because the great scientist’s life spanned 90 years, which saw substantial developments in astronomy) the universe, though considered almost unimaginably massive, was calculated to be much smaller than today’s reckoning. According to a diagram in Man’s Place in the Universe, it ended a little outside the Milky Way galaxy, because we had no tools at the time to measure any further, though Lord Kelvin, the dominant figure in physics and astronomy in the late 19th century, made a number of dodgy calculations that were taken seriously at the time. In fact, Kelvin’s figures for the size of the universe, and for the age of the earth, though too small by orders of magnitude, were considered outrageously huge by most of his contemporaries; but they at least began to accustom the educated public to the idea of ginormity in space and time.

But size wasn’t of course the only thing that made the universe of that time so different from our own conceptions. The universe of Wallace’s imagination was stable, timeless, and, to Wallace’s mind, lifeless, apart of course from our planet. However, he doesn’t appear to have any good argument for this, only improbability. And an odd kind of hope, that we are unique. This hope is revealed in a passage of his book where he goes off the scientific rails just a bit, in a paean to our gloriously unique humanity. A plurality of intelligent life-forms in the universe

… would imply that to produce the living soul in the marvellous and glorious body of man – man with his faculties, his aspirations, his powers for good and evil – that this was an easy matter which could be brought about anywhere, in any world. It would imply man is an animal and nothing more, is of no importance in the universe, needed no great preparations for his advent, only, perhaps, a second-rate demon, and a third or fourth-rate earth.

Wallace, though by no means Christian, was given to ‘spiritualism’, souls and the supernatural, all in relation to humans exclusively. That’s to say, he was wedded to ‘human specialness’, somewhat surprisingly for his theory of evolution by wholly natural selection from random variation. This is the chain, it seems, that links him to modern clingers-to the anthropic principle, such as William Lane Craig and his epigones, who must needs believe in a value-laden universe, with their god as the source of value, and we humans, platonically created as the feeble facsimiles of the godhead, struggling to achieve enlightenment in the form of closeness to the Creator, with its appropriate heavenly rewards. And so we have such typical WL Craigisms as ‘God is the best explanation of moral agents who apprehend necessary moral truths’, ‘God is the best explanation of why there are self-aware beings’ and ‘God is the best explanation of the discoverability of the universe [by humans of course]’. These best explanation ‘arguments’ can be added to ad nauseum, of course, for they’re all of a part, and all connected to the Wallace quote above. We’re special, we must be special, we must be central to the creator’s plan, and our amazingness, our so-much-more-than-animalness, in spite of our many flaws, suggests a truly amazing creator, who made all this just for us.

That’s the hope, captured well by the great French biologist Jaques Monod when he wrote

All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its contingency.

I think modern philosophy has largely moved on from desperate denialism, but Monod’s remarks certainly hold true for religions, past present and future. Basically, the denial of our contingency is the central business of religion. It’s hardly surprising then that the relationship between religion and science is uneasy at best, and antagonistic at its heart. The multiverse could surely be described as religion’s worst nightmare. But that’s another story.